Schema for Drosophila Chain/Net - Drosophila Genomes, Chain and Net Alignments

Database: dm6 Primary Table: netDmirGB2 Row Count: 235,628 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`level`	1	`int(10) unsigned`	range
`tName`	chr2L	`varchar(255)`	values
`tStart`	8733	`int(10) unsigned`	range
`tEnd`	9282	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`qName`	CM001516	`varchar(255)`	values
`qStart`	12024891	`int(10) unsigned`	range
`qEnd`	12025440	`int(10) unsigned`	range
`chainId`	4728	`int(10) unsigned`	range
`ali`	549	`int(10) unsigned`	range
`score`	19926	`double`	range
`qOver`	-1	`int(11)`	range
`qFar`	-1	`int(11)`	range
`qDup`	549	`int(11)`	range
`type`	top	`varchar(255)`	values
`tN`	0	`int(11)`	range
`qN`	0	`int(11)`	range
`tR`	0	`int(11)`	range
`qR`	0	`int(11)`	range
`tNewR`	-1	`int(11)`	range
`qNewR`	-1	`int(11)`	range
`tOldR`	-1	`int(11)`	range
`qOldR`	-1	`int(11)`	range
`tTrf`	0	`int(11)`	range
`qTrf`	0	`int(11)`	range

Sample Rows

bin	level	tName	tStart	tEnd	strand	qName	qStart	qEnd	chainId	ali	score	qOver	qFar	qDup	type	qN	tR	qR	tNewR	qNewR	tOldR	qOldR	tTrf	qTrf
585	1	chr2L	8733	9282	-	CM001516	12024891	12025440	4728	549	19926	-1	-1	549	top	0	0	0	-1	-1	-1	-1	0	0
585	1	chr2L	11214	117977	+	CM001520	28540902	28669921	151	42997	2092689	-1	-1	0	top	190	8407	10305	-1	-1	-1	-1	497	1362
585	2	chr2L	11522	11772	+	CM001520	28541218	28541632	0	0	0	-1	-1	-1	gap	0	0	46	-1	-1	-1	-1	0	0
585	2	chr2L	12936	13515	+	CM001520	28542807	28542865	0	0	0	-1	-1	-1	gap	0	57	0	-1	-1	-1	-1	0	0
585	2	chr2L	15725	17048	+	CM001520	28545085	28547149	0	0	0	-1	-1	-1	gap	0	93	76	-1	-1	-1	-1	0	0
585	2	chr2L	17141	22113	+	CM001520	28547242	28550280	0	0	0	-1	-1	-1	gap	0	0	710	-1	-1	-1	-1	0	0
585	2	chr2L	22944	22988	+	CM001520	28551118	28551195	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	24217	24734	+	CM001520	28552425	28552468	0	0	0	-1	-1	-1	gap	0	249	0	-1	-1	-1	-1	0	0
585	2	chr2L	25070	25988	+	CM001520	28552804	28553976	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0
585	2	chr2L	26068	26282	+	CM001520	28554055	28554309	0	0	0	-1	-1	-1	gap	0	0	0	-1	-1	-1	-1	0	0

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Drosophila Chain/Net (drosophilaChainNet) Track Description


	Description Genomic scaffolds from each Drosophila species are aligned against the D. melanogaster genome assembly (dm6) using LAST with default parameters. The alignments are then processed using the UCSC whole genome alignment protocol (i.e. chaining and netting). References Chain/Net Kent WJ, Baertsch R, Hinrichs A, Miller W, and Haussler D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 2003 100(20): 11484-11489. LAST Kielbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 Mar;21(3):487-93.

Description